<?php 
/**
 * Copyright (c) 2010, Slawomir Mazur <mazursllawek@gmail.com>
 * 
 * All rights reserved.
 * 
 * Redistribution and use in source and binary forms, with or without
 * modification, are permitted provided that the following conditions 
 * are met:
 * 
 * o Redistributions of source code must retain the above copyright notice, 
 *   this list of conditions and the following disclaimer.
 * o Redistributions in binary form must reproduce the above copyright notice,
 *   this list of conditions and the following disclaimer in the documentation
 *   and/or other materials provided with the distribution.
 * o Neither the name of the Softisland nor the names of its contributors
 *   may be used to endorse or promote products derived from this software
 *   without specific prior written permission.
 *
 * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS 
 * "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT 
 * LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR 
 * A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT 
 * HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, 
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 * LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, 
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/**
 * Enter description here...
 *
 * @package     Cms
 * @copyright   Slawomir Mazur (c) 2010 (http://www.zend.com/zce.php?c=ZEND011643)
 * @license     http://www.opensource.org/licenses/bsd-license.php
 * @author      Slawomir Mazur <mazursllawek@gmail.com>
 */
?>

<div class="container">
	<h2>About</h2>
	<div class="content">
		<p>
		RNAiAtlas provides a siRNA oligonucleotide data from different sources and companies like Dharmacon (ThermoFisher), 
		Qiagen, Ambion, esiRNA  for human, and visualize  interactions between siRNA oligo and predicted off-target.
		</p>
		
		<p>
		RNAiAtlas allows to find in genome-wide scale specific siRNA information (sequence and metadata) related to target Gene (search possibility). RNAiAtlas is regulary updated according to RNAi new annotation provided by RNAi suppliers and updated based on Bioinformatics databases. RNAiAtlas, gives an opportunity to navigate between different annotation versions of specific siRNA.
		</p>
		
		<p>
		The occurrence of off-target effects is still a challenging aspect in the interpretation of data from large-scale RNA interference screens. To reduce off-target effects, improved algorithms have been developed for siRNA design, and chemical modifications have been implemented into the double stranded RNA molecule. Still, off-target effects cannot be avoided. Here, we present a bioinformatics database for the representation of predicted  off-target effects that can be applied to large scale RNAi experiments. Our approach provides possibilities to search for specific Gene, siRNA and find predicted off-target information collected from different sources: prediction, TargetScan, existing databses.
		</p>
		
		<p>
		On target analysis is based on siRNA Sequence full match to mRNA transcripts <a class="popup-link" href="http://www.ncbi.nlm.nih.gov/RefSeq/">RefSeq</a> of specific target gene.<br />
		On-target analysis detect following errors in design and annotation
		<img class="diagram" width="900" alt="Diagram" src="<?php echo $this->baseUrl('skin/images/oligo0.png') ?>" />
		<img class="diagram" width="900" alt="Diagram" src="<?php echo $this->baseUrl('skin/images/oligo1.png') ?>" />
		</p>
		
		<p>
		On target analysis is based on siRNA Sequence full match to mRNA transcripts of specific target gene.<br />
		Off-target analysis is based on algorithm:
		<img class="diagram" alt="Diagram" src="<?php echo $this->baseUrl('skin/images/oligo2.gif') ?>" />
		<img class="diagram" alt="Diagram" src="<?php echo $this->baseUrl('skin/images/oligo3.gif') ?>" />
		</p>
		
		<p>
		RNAiAtlas is being develop at LMC-RSC, ETHz Zurich for more information see <a href="<?php echo $this->baseUrl('index/contact') ?>" title="Contact">contact</a>.
		</p>
	</div>
</div>
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